Taking consequences into consideration is not the same thing as consequentialist ethics.

Likewise, some critics talk as though the end never justifies the means. But that's an overstatement.

2. Truman and his war cabinet weren't ethicists, so it's quite possible that their stated justification for dropping the bomb was morally deficient. That doesn't entail that the action itself was wrong. People can think and do the right thing even if they lack the sophistication to make a philosophically solid case for their actions and beliefs.

3. When Japan attacked Pearl Harbor, it forfeited the right not to be attacked. It's actions made it morally liable to counterattack. So it's not just a question of consequences. There's a just cause in play.

4. What alternatives were there to not dropping the bomb?

i) We could refuse to retaliate after the Pearl Harbor attack. But only a pacifist would say that's the right response.

ii) We could try to starve the leadership into submission through a navel blockade. But that would result in mass starvation of noncombatants, as well as POWs. How can you oppose the bombing on the grounds that it violated the immunity of noncombatants if your alternative is starving millions of noncombatants?

iii) We could have chosen not to attack the main island, because the options were so onerous. However, we sustained casualties in Saipan, Leyte, the Philippines, Iwo Jima, and Okinawa. So by that stage it was too late to give up. We were committed to finish the job. If we left Japan undefeated, our soldiers would have died in vain (not to mention the wounded).

5. That leaves us with invasion, which would have resulted in massive casualties for American troops.

Now, the immunity of noncombatants presupposes that killing noncombatants is worse than killing combatants. But is that a morally tenable generalization?

Suppose you have a Marine and a Nazi scientist with the same rare blood type. Suppose both need a life-saving blood transfusion, but there's only enough donated blood on hand to transfuse one of them. Whose life should you save: the combatant (Marine) or the noncombatant (Nazi scientist)? If we are morally discriminating, there are cases in which the death of a combatant is worse than the death of a noncombatant.

Assuming the Americans were fighting for a just case, desire to minimize death and injury to American soldiers is a morally legitimate consideration. Their combatant status doesn't automatically demote the value of their lives in relation to enemy noncombatants. Not to mention that the Japanese gov't was planning to mobilize armed civilian resistance in case of invasion.